Journals in DBLP
Micah Hamady , Erin Peden , Rob Knight , Ravinder Singh Fast-Find: A novel computational approach to analyzing combinatorial motifs. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:1- [Journal ] Pall F. Jonsson , Tamara Cavanna , Daniel Zicha , Paul A. Bates Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:2- [Journal ] Ramón Díaz-Uriarte , Sara Alvarez de Andrés Gene selection and classification of microarray data using random forest. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:3- [Journal ] Lakshmi K. Matukumalli , John J. Grefenstette , David L. Hyten , Ik-Young Choi , Perry B. Cregan , Curtis P. Van Tassell Application of machine learning in SNP discovery. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:4- [Journal ] Heladia Salgado , Alberto Santos-Zavaleta , Socorro Gama-Castro , Martín Peralta-Gil , Mónica I. Peñaloza-Spínola , Agustino Martínez-Antonio , Peter D. Karp , Julio Collado-Vides The comprehensive updated regulatory network of Escherichia coli K-12. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:5- [Journal ] Giacomo Gamberoni , Sergio Storari , Stefano Volinia Finding biological process modifications in cancer tissues by mining gene expression correlations. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:6- [Journal ] Jie Zheng , Jan T. Svensson , Kavitha Madishetty , Timothy J. Close , Tao Jiang , Stefano Lonardi OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:7- [Journal ] Staal A. Vinterbo , Stephan Dreiseitl , Lucila Ohno-Machado Approximation properties of haplotype tagging. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:8- [Journal ] Feng-Biao Guo , Chun-Ting Zhang ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:9- [Journal ] James A. Casbon , Gavin E. Crooks , Mansoor A. S. Saqi A high level interface to SCOP and ASTRAL implemented in Python. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:10- [Journal ] Andrean Goede , Elke Michalsky , Ulrike Schmidt , Robert Preissner SuperMimic - Fitting peptide mimetics into protein structures. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:11- [Journal ] Zihua Hu , Gail R. Willsky Utilization of two sample t -test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:12- [Journal ] Feng Li , Maoyu Li , Zhiqiang Xiao , Pengfei Zhang , Jianling Li , Zhuchu Chen Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML Database - Xindice. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:13- [Journal ] Oliver Sander , Ingolf Sommer , Thomas Lengauer Local protein structure prediction using discriminative models. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:14- [Journal ] James J. Yang , Mark C. K. Yang An improved procedure for gene selection from microarray experiments using false discovery rate criterion. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:15- [Journal ] Markus Brameier , Josien Haan , Andrea Krings , Robert M. MacCallum Automatic discovery of cross-family sequence features associated with protein function. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:16- [Journal ] Brian Tjaden An approach for clustering gene expression data with error information. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:17- [Journal ] Yuan-Yuan Li , Lei Qin , Zong-Ming Guo , Lei Liu , Hao Xu , Pei Hao , Jiong Su , Yixiang Shi , Wei-Zhong He , Yi-Xue Li In silico discovery of human natural antisense transcripts. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:18- [Journal ] Morgan N. Price , Adam P. Arkin , Eric J. Alm OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:19- [Journal ] Youfang Cao , Shi Liu , Lida Zhang , Jie Qin , Jiang Wang , Kexuan Tang Prediction of protein structural class with Rough Sets. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:20- [Journal ] Patrick Durand , Laurent Labarre , Alain Meil , Jean-Louis Divol , Yves Vandenbrouck , Alain Viari , Jérôme Wojcik GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:21- [Journal ] Alexei A. Adzhubei , Jon K. Laerdahl , Anna V. Vlasova preAssemble: a tool for automatic sequencer trace data processing. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:22- [Journal ] Li-Xuan Qin , Richard P. Beyer , Francesca N. Hudson , Nancy J. Linford , Daryl E. Morris , Kathleen F. Kerr Evaluation of methods for oligonucleotide array data via quantitative real-time PCR. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:23- [Journal ] Kyaw Tun , Pawan K. Dhar , Maria Concetta Palumbo , Alessandro Giuliani Metabolic pathways variability and sequence/networks comparisons. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:24- [Journal ] Jason C. Ting , Ying Ye , George H. Thomas , Ingo Ruczinski , Jonathan Pevsner Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:25- [Journal ] Xia Li , Shaoqi Rao , Wei Jiang , Chuanxing Li , Yun Xiao , Zheng Guo , Qingpu Zhang , Lihong Wang , Lei Du , Jing Li , Li Li , Tianwen Zhang , Qing K. Wang Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:26- [Journal ] Hongbo Zhu , Francisco S. Domingues , Ingolf Sommer , Thomas Lengauer NOXclass: prediction of protein-protein interaction types. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:27- [Journal ] Nicolas Thierry-Mieg A new pooling strategy for high-throughput screening: the Shifted Transversal Design. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:28- [Journal ] Thomas Mailund , Gerth Stølting Brodal , Rolf Fagerberg , Christian N. S. Pedersen , Derek Phillips Recrafting the neighbor-joining method. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:29- [Journal ] Ming Yi , Jay D. Horton , Jonathan C. Cohen , Helen H. Hobbs , Robert M. Stephens WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:30- [Journal ] Bradford C. Powell , Clyde A. Hutchison III Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:31- [Journal ] Xian Wang , Ao Li , Zhaohui Jiang , Huanqing Feng Missing value estimation for DNA microarray gene expression data by Support Vector Regression imputation and orthogonal coding scheme. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:32- [Journal ] Erdahl T. Teber , Edward Crawford , Kent B. Bolton , Derek Van Dyk , Peter R. Schofield , Vimal Kapoor , W. Bret Church Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:33- [Journal ] Holger Conzelmann , Julio Saez-Rodriguez , Thomas Sauter , Boris N. Kholodenko , Ernst Dieter Gilles A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:34- [Journal ] Kyoungmi Kim , Grier P. Page , T. Mark Beasley , Stephen Barnes , Katherine E. Scheirer , David B. Allison A proposed metric for assessing the measurement quality of individual microarrays. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:35- [Journal ] Domenico Catalano , Flavio Licciulli , Antonio Turi , Giorgio Grillo , Cecilia Saccone , Domenica D'Elia MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:36- [Journal ] Xiao I. Liu , Neeraj Korde , Ursula Jakob , Lars I. Leichert CoSMoS: Conserved Sequence Motif Search in the proteome. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:37- [Journal ] Hao-Teng Chang , Tun-Wen Pai , Tan-Chi Fan , Bo-Han Su , Pei-Chih Wu , Chuan Yi Tang , Chun-Tien Chang , Shi-Hwei Liu , Margaret Dah-Tsyr Chang A reinforced merging methodology for mapping unique peptide motifs in members of protein families. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:38- [Journal ] Alison A. Motsinger , Stephen L. Lee , George Mellick , Marylyn D. Ritchie GPNN: Power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:39- [Journal ] Xiaobo Zhou , James Chou , Stephen T. C. Wong Protein structure similarity from principle component correlation analysis. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:40- [Journal ] Monica Chagoyen , Pedro Carmona-Saez , Hagit Shatkay , José María Carazo , Alberto D. Pascual-Montano Discovering semantic features in the literature: a foundation for building functional associations. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:41- [Journal ] Harald Barsnes , Svein-Ole Mikalsen , Ingvar Eidhammer MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:42- [Journal ] Tim Van den Bulcke , Koen Van Leemput , Bart Naudts , Piet van Remortel , Hongwu Ma , Alain Verschoren , Bart De Moor , Kathleen Marchal SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:43- [Journal ] Ryung S. Kim , Hongkai Ji , Wing Hung Wong An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:44- [Journal ] Olivier Croce , Michaël Lamarre , Richard Christen Querying the public databases for sequences using complex keywords contained in the feature lines. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:45- [Journal ] Wen-Yu Chung , Réka Albert , István Albert , Anton Nekrutenko , Kateryna D. Makova Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:46- [Journal ] Ross I. Brinkworth , Alan L. Munn , Bostjan Kobe Protein kinases associated with the yeast phosphoproteome. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:47- [Journal ] James A. Casbon , Mansoor A. S. Saqi On single and multiple models of protein families for the detection of remote sequence relationships. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:48- [Journal ] Jeanette N. McClintick , Howard J. Edenberg Effects of filtering by Present call on analysis of microarray experiments. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:49- [Journal ] Xing Qiu , Yuanhui Xiao , Alexander Gordon , Andrei Yakovlev Assessing stability of gene selection in microarray data analysis. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:50- [Journal ] Kristofer Hallén , Johan Björkegren , Jesper Tegnér Detection of compound mode of action by computational integration of whole-genome measurements and genetic perturbations. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:51- [Journal ] Bor-Sen Chen , Yu-Chao Wang On the attenuation and amplification of molecular noise in genetic regulatory networks. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:52- [Journal ] Marcin von Grotthuss , Dariusz Plewczynski , Krzysztof Ginalski , Leszek Rychlewski , Eugene I. Shakhnovich PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:53- [Journal ] Pedro Carmona-Saez , Monica Chagoyen , Andrés Rodríguez , Oswaldo Trelles , José María Carazo , Alberto D. Pascual-Montano Integrated analysis of gene expression by association rules discovery. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:54- [Journal ] Michael Baitaluk , Xufei Qian , Shubhada Godbole , Alpan Raval , Animesh Ray , Amarnath Gupta PathSys: integrating molecular interaction graphs for systems biology. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:55- [Journal ] Steffen Klamt , Julio Saez-Rodriguez , Jonathan A. Lindquist , Luca Simeoni , Ernst Dieter Gilles A methodology for the structural and functional analysis of signaling and regulatory networks. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:56- [Journal ] Yanan Yu , Mya Breitbart , Pat McNairnie , Forest Rohwer FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:57- [Journal ] Bin Zheng , David C. McLean Jr , Xinghua Lu Identifying biological concepts from a protein-related corpus with a probabilistic topic model. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:58- [Journal ] Hemant Ishwaran , J. Sunil Rao , Udaya B. Kogalur BAMarrayTM : Java software for Bayesian analysis of variance for microarray data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:59- [Journal ] Kim W. Carter , Pamela A. McCaskie , Lyle J. Palmer JLIN: A java based linkage disequilibrium plotter. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:60- [Journal ] Phillip McClurg , Mathew T. Pletcher , Tim Wiltshire , Andrew I. Su Comparative analysis of haplotype association mapping algorithms. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:61- [Journal ] Mario Stanke , Oliver Schöffmann , Burkhard Morgenstern , Stephan Waack Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:62- [Journal ] Claes R. Andersson , Anders Isaksson , Mats G. Gustafsson Bayesian detection of periodic mRNA time profiles without use of training examples. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:63- [Journal ] Christoph Gille , Peter N. Robinson HotSwap for bioinformatics: A STRAP tutorial. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:64- [Journal ] Svetlana A. Shabalina , Alexey N. Spiridonov , Aleksey Y. Ogurtsov Computational models with thermodynamic and composition features improve siRNA design. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:65- [Journal ] Hanno Teeling , Frank Oliver Glöckner RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:66- [Journal ] Christian V. Forst , Christoph Flamm , Ivo L. Hofacker , Peter F. Stadler Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:67- [Journal ] Mikael Bodén , Zheng Yuan , Timothy L. Bailey Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:68- [Journal ] Feng He , An-Ping Zeng In search of functional association from time-series microarray data based on the change trend and level of gene expression. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:69- [Journal ] Aaron Birkland , Golan Yona BIOZON: a system for unification, management and analysis of heterogeneous biological data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:70- [Journal ] Paul Shafer , Timothy Isganitis , Golan Yona Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:71- [Journal ] Zuozhou Chen , Weilin Wang , Xuefeng Bruce Ling , Jane Jijun Liu , Liangbiao Chen GO-Diff: Mining functional differentiation between EST-based transcriptomes. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:72- [Journal ] Daniel P. Berrar , Ian Bradbury , Werner Dubitzky Instance-based concept learning from multiclass DNA microarray data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:73- [Journal ] Brandon W. Higgs , Jennifer W. Weller , Jeffrey L. Solka Spectral embedding finds meaningful (relevant) structure in image and microarray data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:74- [Journal ] Andrew E. Firth , Chris M. Brown Detecting overlapping coding sequences in virus genomes. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:75- [Journal ] Chengpeng Bi , Peter K. Rogan BIPAD: A web server for modeling bipartite sequence elements. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:76- [Journal ] Donglin Liu , Joel H. Graber Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:77- [Journal ] Pedro Carmona-Saez , Roberto D. Pascual-Marqui , Francisco Tirado , José María Carazo , Alberto D. Pascual-Montano Biclustering of gene expression data by non-smooth non-negative matrix factorization. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:78- [Journal ] Gareth Palidwor , Emmanuel G. Reynaud , Miguel A. Andrade-Navarro Taxonomic colouring of phylogenetic trees of protein sequences. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:79- [Journal ] Jie Wu , Zhenjun Hu , Charles DeLisi Gene annotation and network inference by phylogenetic profiling. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:80- [Journal ] Alistair R. R. Forrest , Darrin F. Taylor , J. Lynn Fink , M. Milena Gongora , Cameron Flegg , Rohan D. Teasdale , Harukazu Suzuki , Mutsumi Kanamori , Chikatoshi Kai , Yoshihide Hayashizaki , Sean M. Grimmond PhosphoregDB: The tissue and sub-cellular distribution of mammalian protein kinases and phosphatases. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:82- [Journal ] Jing Huang , Wen Wei , Joyce Chen , Jane Zhang , Guoying Liu , Xiaojun Di , Rui Mei , Shumpei Ishikawa , Hiroyuki Aburatani , Keith W. Jones , Michael H. Shapero CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:83- [Journal ] Grier P. Page , Jode W. Edwards , Gary L. Gadbury , Prashanth Yelisetti , Jelai Wang , Prinal Trivedi , David B. Allison The PowerAtlas : a power and sample size atlas for microarray experimental design and research. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:84- [Journal ] Joshua S. Yuan , Ann Reed , Feng Chen , C. Neal Stewart Jr. Statistical analysis of real-time PCR data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:85- [Journal ] Ricardo Z. N. Vêncio , Tie Koide , Suely L. Gomes , Carlos A. de B. Pereira BayGO: Bayesian analysis of ontology term enrichment in microarray data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:86- [Journal ] Delong Liu , Shyamal D. Peddada , Leping Li , Clarice R. Weinberg Phase analysis of circadian-related genes in two tissues. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:87- [Journal ] Jonathan P. Bollback SIMMAP: Stochastic character mapping of discrete traits on phylogenies. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:88- [Journal ] Michael E. Bradley , Steven A. Benner Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:89- [Journal ] Shann-Ching Chen , Robert F. Murphy A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:90- [Journal ] Sudhir Varma , Richard Simon Bias in error estimation when using cross-validation for model selection. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:91- [Journal ] Richard Tzong-Han Tsai , Shih-Hung Wu , Wen-Chi Chou , Yu-Chun Lin , Ding He , Jieh Hsiang , Ting-Yi Sung , Wen-Lian Hsu Various criteria in the evaluation of biomedical named entity recognition. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:92- [Journal ] Howard Salis , Vassilios Sotiropoulos , Yiannis N. Kaznessis Multiscale Hy3S: Hybrid stochastic simulation for supercomputers. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:93- [Journal ] Stefan M. Stanley , Timothy L. Bailey , John S. Mattick GONOME: measuring correlations between GO terms and genomic positions. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:94- [Journal ] E. Ke Tang , Ponnuthurai N. Suganthan , Xin Yao Gene selection algorithms for microarray data based on least squares support vector machine. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:95- [Journal ] Anders Bengtsson , Henrik Bengtsson Microarray image analysis: background estimation using quantile and morphological filters. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:96- [Journal ] Richard G. Côté , Philip Jones , Rolf Apweiler , Henning Hermjakob The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:97- [Journal ] Patrick Martin , Kim E. Boulukos , Philippe Pognonec REtools: A laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:98- [Journal ] Ghislain Bidaut , Karsten Suhre , Jean-Michel Claverie , Michael F. Ochs Determination of strongly overlapping signaling activity from microarray data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:99- [Journal ] Henrik Bengtsson , Ola Hössjer Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:100- [Journal ] Yian A. Chen , Cheng-Chung Chou , Xinghua Lu , Elizabeth H. Slate , Konan Peck , Wenying Xu , Eberhard O. Voit , Jonas S. Almeida A multivariate prediction model for microarray cross-hybridization. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:101- [Journal ] Richard P. Auburn , Roslin R. Russell , Bettina Fischer , Lisa A. Meadows , Santiago Sevillano Matilla , Steven Russell SimArray: a user-friendly and user-configurable microarray design tool. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:102- [Journal ] Arthur Chun-Chieh Shih , D. T. Lee , Laurent Lin , Chin-Lin Peng , Shiang-Heng Chen , Yu-Wei Wu , Chun-Yi Wong , Meng-Yuan Chou , Tze-Chang Shiao , Mu-Fen Hsieh SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:103- [Journal ] Joan Teyra , Andreas Doms , Michael Schroeder , M. Teresa Pisabarro SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:104- [Journal ] Robert Tibshirani A simple method for assessing sample sizes in microarray experiments. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:106- [Journal ] Rasmus Goll , Trine Olsen , Guanglin Cui , Jon Florholmen Evaluation of absolute quantitation by nonlinear regression in probe-based real-time PCR. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:107- [Journal ] Teresa W. Haynes , Debra J. Knisley , Edith Seier , Yue Zou A quantitative analysis of secondary RNA structure using domination based parameters on trees. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:108- [Journal ] Björn H. Junker , Christian Klukas , Falk Schreiber VANTED: A system for advanced data analysis and visualization in the context of biological networks. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:109- [Journal ] Michael Spitzer , Stefan Lorkowski , Paul Cullen , Alexander Sczyrba , Georg Fuellen IsoSVM - Distinguishing isoforms and paralogs on the protein level. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:110- [Journal ] Scott A. Becker , Nathan D. Price , Bernhard O. Palsson Metabolite coupling in genome-scale metabolic networks. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:111- [Journal ] Hidenori Inaoka , Yutaka Fukuoka , Isaac S. Kohane Lower expression of genes near microRNA in C. elegans germline. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:112- [Journal ] Kenzie D. MacIsaac , Ting Wang , D. Benjamin Gordon , David K. Gifford , Gary D. Stormo , Ernest Fraenkel An improved map of conserved regulatory sites for Saccharomyces cerevisiae . [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:113- [Journal ] Victor X. Jin , Gregory A. Singer , Francisco J. Agosto-Perez , Sandya Liyanarachchi , Ramana V. Davuluri Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:114- [Journal ] Chun Liang , Feng Sun , Haiming Wang , Junfeng Qu , Robert M. Freeman Jr , Lee H. Pratt , Marie-Michèle Cordonnier-Pratt MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:115- [Journal ] Haiying Wang , Huiru Zheng , David Simpson , Francisco Azuaje Machine learning approaches to supporting the identification of photoreceptor-enriched genes based on expression data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:116- [Journal ] Zhengdong Zhang , George W. Jackson , George E. Fox , Richard C. Willson Microbial identification by mass cataloging. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:117- [Journal ] Areejit Samal , Shalini Singh , Varun Giri , Sandeep Krishna , Nandula Raghuram , Sanjay Jain Low degree metabolites explain essential reactions and enhance modularity in biological networks. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:118- [Journal ] Rainer König , Gunnar Schramm , Marcus Oswald , Hanna Seitz , Sebastian Sager , Marc Zapatka , Gerhard Reinelt , Roland Eils Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:119- [Journal ] Sebastiaan Horsman , Michael J. Moorhouse , Victor C. L. de Jager , Peter van der Spek , Frank Grosveld , John Strouboulis , Eleni Z. Katsantoni TF Target Mapper: A BLAST search tool for the identification of Transcription Factor target genes. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:120- [Journal ] Maike Tech , Peter Meinicke An unsupervised classification scheme for improving predictions of prokaryotic TIS. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:121- [Journal ] Xiaochen Bo , Shaoke Lou , Daochun Sun , Wenjie Shu , Jing Yang , Shengqi Wang Selection of antisense oligonucleotides based on multiple predicted target mRNA structures. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:122- [Journal ] Harvey J. Motulsky , Ronald E. Brown Detecting outliers when fitting data with nonlinear regression - a new method based on robust nonlinear regression and the false discovery rate. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:123- [Journal ] Jiangning Song , Kevin Burrage , Zheng Yuan , Thomas Huber Prediction of cis /trans isomerization in proteins using PSI-BLAST profiles and secondary structure information. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:124- [Journal ] Michael Meissner , Michael Schmuker , Gisbert Schneider Optimized Particle Swarm Optimization (OPSO) and its application to artificial neural network training. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:125- [Journal ] Richard J. Fox , Matthew W. Dimmic A two-sample Bayesian t -test for microarray data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:126- [Journal ] Ulrika Wickenberg-Bolin , Hanna Göransson , Mårten Fryknäs , Mats G. Gustafsson , Anders Isaksson Improved variance estimation of classification performance via reduction of bias caused by small sample size. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:127- [Journal ] Ramazan Saeed , Charlotte M. Deane Protein protein interactions, evolutionary rate, abundance and age. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:128- [Journal ] Robert Urbanczik SNA - a toolbox for the stoichiometric analysis of metabolic networks. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:129- [Journal ] Takuji Yamada , Minoru Kanehisa , Susumu Goto Extraction of phylogenetic network modules from the metabolic network. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:130- [Journal ] Irini A. Doytchinova , Pingping Guan , Darren R. Flower EpiJen: a server for multistep T cell epitope prediction. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:131- [Journal ] Christian L. Barrett , Nathan D. Price , Bernhard O. Palsson Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:132- [Journal ] Yanni Sun , Jeremy Buhler Choosing the best heuristic for seeded alignment of DNA sequences. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:133- [Journal ] Seo Young Kim , Jae Won Lee , Jong Sung Bae Effect of data normalization on fuzzy clustering of DNA microarray data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:134- [Journal ] Feng-Chi Chen , Chuang-Jong Chen , Jar-Yi Ho , Trees-Juen Chuang Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:136- [Journal ] Frank F. Millenaar , John Okyere , Sean T. May , Martijn van Zanten , Laurentius A. C. J. Voesenek , Anton J. M. Peeters How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:137- [Journal ] Min Lin , Rongling Wu A joint model for nonparametric functional mapping of longitudinal trajectory and time-to-event. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:138- [Journal ] Yuliya V. Karpievitch , Jonas S. Almeida mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:139- [Journal ] Minsuk Lee , Weiqing Wang , Hong Yu Exploring supervised and unsupervised methods to detect topics in biomedical text. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:140- [Journal ] Tilman Lamparter A computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:141- [Journal ] Stephan Waack , Oliver Keller , Roman Asper , Thomas Brodag , Carsten Damm , Wolfgang Florian Fricke , Katharina Surovcik , Peter Meinicke , Rainer Merkl Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:142- [Journal ] Rahul Siddharthan Sigma: multiple alignment of weakly-conserved non-coding DNA sequence. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:143- [Journal ] Markus Seiler , Alexander Mehrle , Annemarie Poustka , Stefan Wiemann The 3of5 web application for complex and comprehensive pattern matching in protein sequences. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:144- [Journal ] James Thompson , Shuba Gopal Genetic algorithm learning as a robust approach to RNA editing site prediction. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:145- [Journal ] Aaron N. Chang , Jason McDermott , Zachary Frazier , Michal Guerquin , Ram Samudrala INTEGRATOR: interactive graphical search of large protein interactomes over the Web. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:146- [Journal ] J. R. Semeiks , A. Rizki , Mina J. Bissell , I. Saira Mian Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:147- [Journal ] Wendy S. W. Wong , Raazesh Sainudiin , Rasmus Nielsen Identification of physicochemical selective pressure on protein encoding nucleotide sequences. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:148- [Journal ] Kevin A. Greer , Matthew R. McReynolds , Heddwen L. Brooks , James B. Hoying CARMA: A platform for analyzing microarray datasets that incorporate replicate measures. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:149- [Journal ] Colleen D. Behrsin , Chris J. Brandl , David W. Litchfield , Brian H. Shilton , Lindi M. Wahl Development of an unbiased statistical method for the analysis of unigenic evolution. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:150- [Journal ] Jason M. Doherty , Lynn K. Carmichael , Jason C. Mills GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:151- [Journal ] Kevin A. Snyder , Howard J. Feldman , Michel Dumontier , John J. Salama , Christopher W. V. Hogue Domain-based small molecule binding site annotation. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:152- [Journal ] Huynh-Hoa Bui , John Sidney , Kenny Dinh , Scott Southwood , Mark J. Newman , Alessandro Sette Predicting population coverage of T-cell epitope-based diagnostics and vaccines. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:153- [Journal ] Richard E. Kennedy , Kellie J. Archer , Michael F. Miles Empirical validation of the S-Score algorithm in the analysis of gene expression data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:154- [Journal ] Erik Arner , Martti T. Tammi , Anh-Nhi Tran , Ellen Kindlund , Björn Andersson DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:155- [Journal ] Shigeyuki Matsui Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:156- [Journal ] Helene H. Thygesen , Aeilko H. Zwinderman Modeling Sage data with a truncated gamma-Poisson model. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:157- [Journal ] Lars Malmström , György Marko-Varga , Gunilla Westergren-Thorsson , Thomas Laurell , Johan Malmström 2DDB - a bioinformatics solution for analysis of quantitative proteomics data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:158- [Journal ] Enrique M. Muro , Carolina Perez-Iratxeta , Miguel A. Andrade-Navarro Amplification of the Gene Ontology annotation of Affymetrix probe sets. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:159- [Journal ] Pieter Monsieurs , Gert Thijs , Abeer A. Fadda , Sigrid C. J. De Keersmaecker , Jozef Vanderleyden , Bart De Moor , Kathleen Marchal More robust detection of motifs in coexpressed genes by using phylogenetic information. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:160- [Journal ] Arunachalam Vinayagam , Coral del Val , Falk Schubert , Roland Eils , Karl-Heinz Glatting , Sándor Suhai , Rainer König GOPET: A tool for automated predictions of Gene Ontology terms. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:161- [Journal ] Beltran Rodriguez-Brito , Forest Rohwer , Robert Edwards An application of statistics to comparative metagenomics. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:162- [Journal ] Yu Xue , Ao Li , Lirong Wang , Huanqing Feng , Xuebiao Yao PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:163- [Journal ] Georg Schneider , Georg Neuberger , Michael Wildpaner , Sun Tian , Igor N. Berezovsky , Frank Eisenhaber Application of a sensitive collection heuristic for very large protein families: Evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:164- [Journal ] Hyunsoo Kim , William Hu , Yuval Kluger Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:165- [Journal ] Peng Yue , Eugene Melamud , John Moult SNPs3D: Candidate gene and SNP selection for association studies. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:166- [Journal ] Peteris Prusis , Staffan Uhlén , Ramona Petrovska , Maris Lapinsh , Jarl E. S. Wikberg Prediction of indirect interactions in proteins. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:167- [Journal ] Kazuharu Arakawa , Yohei Yamada , Kosaku Shinoda , Yoichi Nakayama , Masaru Tomita GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:168- [Journal ] Vincent Le Texier , Jean-Jack M. Riethoven , Vasudev Kumanduri , Chellappa Gopalakrishnan , Fabrice Lopez , Daniel Gautheret , Thangavel Alphonse Thanaraj AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:169- [Journal ] Thomas J. Lee , Yannick Pouliot , Valerie Wagner , Priyanka Gupta , David W. J. Stringer-Calvert , Jessica D. Tenenbaum , Peter D. Karp BioWarehouse: a bioinformatics database warehouse toolkit. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:170- [Journal ] Anton Yuryev , Zufar Mulyukov , Ekaterina Kotelnikova , Sergei Maslov , Sergei Egorov , Alexander Nikitin , Nikolai Daraselia , Ilya Mazo Automatic pathway building in biological association networks. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:171- [Journal ] Reidar Andreson , Eric Reppo , Lauris Kaplinski , Maido Remm GENOMEMASKER package for designing unique genomic PCR primers. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:172- [Journal ] Andrew V. Uzilov , Joshua M. Keegan , David H. Mathews Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:173- [Journal ] Vicente Arnau , Miguel Gallach , J. Ignasi Lucas , Ignacio Marín UVPAR: fast detection of functional shifts in duplicate genes. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:174- [Journal ] Guoli Wang , Andrew V. Kossenkov , Michael F. Ochs LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:175- [Journal ] Paul T. Shannon , David J. Reiss , Richard Bonneau , Nitin S. Baliga The Gaggle: An open-source software system for integrating bioinformatics software and data sources. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:176- [Journal ] Peter Kharchenko , Lifeng Chen , Yoav Freund , Dennis Vitkup , George M. Church Identifying metabolic enzymes with multiple types of association evidence. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:177- [Journal ] Zafer Aydin , Yucel Altunbasak , Mark Borodovsky Protein secondary structure prediction for a single-sequence using hidden semi-Markov models. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:178- [Journal ] Sangjo Han , Dongsup Kim AtRTPrimer: database for Arabidopsis genome-wide homogeneous and specific RT-PCR primer-pairs. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:179- [Journal ] Alessandro Vullo , Ian Walsh , Gianluca Pollastri A two-stage approach for improved prediction of residue contact maps. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:180- [Journal ] Wen Liu , Xiangshan Meng , Qiqi Xu , Darren R. Flower , Tongbin Li Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:182- [Journal ] Veronica Vinciotti , Xiaohui Liu , Rolf Turk , Emile J. de Meijer , Peter A. C. 't Hoen Exploiting the full power of temporal gene expression profiling through a new statistical test: Application to the analysis of muscular dystrophy data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:183- [Journal ] Ester Vilaprinyó , Rui Alves , Albert Sorribas Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:184- [Journal ] H. Alexander Ebhardt , Kay C. Wiese , Peter J. Unrau Ebbie : automated analysis and storage of small RNA cloning data using a dynamic web server. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:185- [Journal ] Jean-Marc Schwartz , Minoru Kanehisa Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:186- [Journal ] Xiaojing Yu , Chuan Wang , Yixue Li Classification of protein quaternary structure by functional domain composition. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:187- [Journal ] Julien Dutheil , Sylvain Gaillard , Eric Bazin , Sylvain Glemin , Vincent Ranwez , Nicolas Galtier , Khalid Belkhir Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:188- [Journal ] Pantelis G. Bagos , Theodore D. Liakopoulos , Stavros J. Hamodrakas Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:189- [Journal ] Leandro Hermida , Olivier Schaad , Philippe Demougin , Patrick Descombes , Michael Primig MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:190- [Journal ] Jason Ernst , Ziv Bar-Joseph STEM: a tool for the analysis of short time series gene expression data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:191- [Journal ] Peter Ruzanov , Steven J. M. Jones An interactive tool for visualization of relationships between gene expression profiles. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:193- [Journal ] Joseph C. Roden , Brandon W. King , Diane Trout , Ali Mortazavi , Barbara J. Wold , Christopher E. Hart Mining gene expression data by interpreting principal components. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:194- [Journal ] Svetlana Pacifico , Guozhen Liu , Stephen Guest , Jodi R. Parrish , Farshad Fotouhi , Russell L. Finley Jr. A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila . [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:195- [Journal ] Stephen A. Racunas , Nigam Shah , Nina V. Fedoroff A case study in pathway knowledgebase verification. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:196- [Journal ] Xuegong Zhang , Xin Lu , Qian Shi , Xiu-qin Xu , Hon-chiu E. Leung , Lyndsay N. Harris , James D. Iglehart , Alexander Miron , Jun S. Liu , Wing Hung Wong Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:197- [Journal ] Werner W. V. B. Van Belle , Nina N. A. Anensen , Ingvild I. H. Haaland , Oystein O. B. Bruserud , Kjell-Arild K. A. H. Hogda , Bjorn B. T. G. Tore Gjertsen Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:198- [Journal ] Tomer Shlomi , Daniel Segal , Eytan Ruppin , Roded Sharan QPath: a method for querying pathways in a protein-protein interaction network. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:199- [Journal ] Rachel I. M. van Haaften , Blanche Schroen , Ben J. A. Janssen , Arie van Erk , Jacques J. M. Debets , Hubert J. M. Smeets , Jos F. M. Smits , Arthur van den Wijngaard , Yigal M. Pinto , Chris T. A. Evelo Biologically relevant effects of mRNA amplification on gene expression profiles. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:200- [Journal ] Paramvir S. Dehal , Jeffrey L. Boore A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:201- [Journal ] Chaolin Zhang , Hai-Ri Li , Jian-Bing Fan , Jessica Wang-Rodriguez , Tracy Downs , Xiang-Dong Fu , Michael Q. Zhang Profiling alternatively spliced mRNA isoforms for prostate cancer classification. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:202- [Journal ] Tricia A. Thornton-Wells , Jason H. Moore , Jonathan L. Haines Dissecting trait heterogeneity: a comparison of three clustering methods applied to genotypic data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:204- [Journal ] Casper J. Albers , Ritsert C. Jansen , Jan Kok , Oscar P. Kuipers , Sacha A. F. T. van Hijum SIMAGE: simulation of DNA-microarray gene expression data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:205- [Journal ] Vichetra Sam , Chin-Hsien Tai , Jean Garnier , Jean-François Gibrat , Byungkook Lee , Peter J. Munson ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:206- [Journal ] Md. Altaf-Ul-Amin , Yoko Shinbo , Kenji Mihara , Ken Kurokawa , Shigehiko Kanaya Development and implementation of an algorithm for detection of protein complexes in large interaction networks. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:207- [Journal ] Kang Peng , Predrag Radivojac , Slobodan Vucetic , A. Keith Dunker , Zoran Obradovic Length-dependent prediction of protein intrinsic disorder. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:208- [Journal ] Kristina Allen-Brady , Jathine Wong , Nicola J. Camp PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:209- [Journal ] Simon Fiddy , David Cattermole , Dong Xie , Xiao Yuan Duan , Richard Mott An integrated system for genetic analysis. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:210- [Journal ] Lesley Jones , Darlene R. Goldstein , Gareth P. Hughes , Andrew Strand , Francois Collin , Stephen B. Dunnett , Charles L. Kooperberg , Aaron Aragaki , James M. Olson , Sarah J. Augood , Richard L. M. Faull , Ruth Luthi-Carter , Valentina Moskvina , Angela K. Hodges Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:211- [Journal ] Jacob Köhler , Katherine Munn , Alexander Rüegg , Andre Skusa , Barry Smith Quality control for terms and definitions in ontologies and taxonomies. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:212- [Journal ] Michael L. Tress , Domenico Cozzetto , Anna Tramontano , Alfonso Valencia An analysis of the Sargasso Sea resource and the consequences for database composition. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:213- [Journal ] Peter Steffen , Robert Giegerich Correction: versatile and declarative dynamic programming using pair algebras. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:214- [Journal ] Allan A. Sioson , Shrinivasrao P. Mane , Pinghua Li , Wei Sha , Lenwood S. Heath , Hans J. Bohnert , Ruth Grene The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:215- [Journal ] Rafal Kustra , Romy Shioda , Mu Zhu A factor analysis model for functional genomics. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:216- [Journal ] Amrita Pati , Cecilia Vasquez-Robinet , Lenwood S. Heath , Ruth Grene , T. M. Murali XcisClique: analysis of regulatory bicliques. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:218- [Journal ] Björn H. Junker , Dirk Koschützki , Falk Schreiber Exploration of biological network centralities with CentiBiN. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:219- [Journal ] Aditya Kumar Sehgal , Padmini Srinivasan Retrieval with gene queries. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:220- [Journal ] Alexander Churkin , Danny Barash RNAmute: RNA secondary structure mutation analysis tool. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:221- [Journal ] Zhuo Zhang , Shiwei Sun , Xiaopeng Zhu , Suhua Chang , Xiaofei Liu , Chungong Yu , Dongbo Bu , Runsheng Chen A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:222- [Journal ] Tong Zhou , Jianhong Weng , Xiao Sun , Zuhong Lu Support vector machine for classification of meiotic recombination hotspots and coldspots in Saccharomyces cerevisiaebased on codon composition. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:223- [Journal ] Thierry-Pascal Baum , Vivien Hierle , Nicolas Pasqual , Fatena Bellahcene , Denys Chaume , Marie-Paule Lefranc , Evelyne Jouvin-Marche , Patrice-Noël Marche , Jacques Demongeot IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:224- [Journal ] Marcin P. Joachimiak , Jennifer L. Weissman , Barnaby C. H. May JColorGrid: software for the visualization of biological measurements. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:225- [Journal ] Filippo Rusconi GNU polyxmass: a software framework for mass spectrometric simulations of linear (bio-)polymeric analytes. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:226- [Journal ] Kun Yang , Zhipeng Cai , Jianzhong Li , Guohui Lin A stable gene selection in microarray data analysis. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:228- [Journal ] Bertrand R. Huber , Martha L. Bulyk Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:229- [Journal ] Yoshiya Matsubara , Shinichi Kikuchi , Masahiro Sugimoto , Masaru Tomita Parameter estimation for stiff equations of biosystems using radial basis function networks. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:230- [Journal ] Paul-Ludwig Lott , Marvin Mundry , Christoph Sassenberg , Stefan Lorkowski , Georg Fuellen Simplifying gene trees for easier comprehension. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:231- [Journal ] Cheng-Chung Chou , Te-Tsui Lee , Chun-Houh Chen , Hsiang-Yun Hsiao , Yi-Ling Lin , Mei-Shang Ho , Pan-Chyr Yang , Konan Peck Design of microarray probes for virus identification and detection of emerging viruses at the genus level. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:232- [Journal ] Hsin-Chou Yang , Chia-Ching Pan , Chin-Yu Lin , Cathy S. J. Fann PDA: Pooled DNA analyzer. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:233- [Journal ] Tobias Kind , Oliver Fiehn Metabolomic database annotations viaquery of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:234- [Journal ] Carmen Lai , Marcel J. T. Reinders , Laura J. van't Veer , Lodewyk F. A. Wessels A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:235- [Journal ] David Tuck , Harriet Kluger , Yuval Kluger Characterizing disease states from topological properties of transcriptional regulatory networks. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:236- [Journal ] Jamie A. Lee , Robert S. Sinkovits , Dennis Mock , Eva L. Rab , Jennifer Cai , Peng Yang , Brian Saunders , Robert C. Hsueh , Sangdun Choi , Shankar Subramaniam , Richard H. Scheuermann Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:237- [Journal ] Yi Lu , Adrian E. Platts , G. Charles Ostermeier , Stephen A. Krawetz K-SPMM: a database of murine spermatogenic promoters modules & motifs. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:238- [Journal ] Kasper Munch , Paul P. Gardner , Peter Arctander , Anders Krogh A hidden Markov model approach for determining expression from genomic tiling micro arrays. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:239- [Journal ] Yadhu Kumar , Ralf Westram , Peter Kipfer , Harald Meier , Wolfgang Ludwig Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:240- [Journal ] Marc Aubry , Annabelle Monnier , Celine Chicault , Marie de Tayrac , Marie-Dominique Galibert , Anita Burgun , Jean Mosser Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:241- [Journal ] Apostol Gramada , Philip E. Bourne Multipolar representation of protein structure. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:242- [Journal ] Jijoy Joseph , Roschen Sasikumar Chaos game representation for comparison of whole genomes. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:243- [Journal ] Mohammad Anwar , Truong Nguyen , Marcel Turcotte Identification of consensus RNA secondary structures using suffix arrays. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:244- [Journal ] Hao Li , Constance L. Wood , Yushu Liu , Thomas V. Getchell , Marilyn L. Getchell , Arnold J. Stromberg Identification of gene expression patterns using planned linear contrasts. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:245- [Journal ] Hiroto Saigo , Jean-Philippe Vert , Tatsuya Akutsu Optimizing amino acid substitution matrices with a local alignment kernel. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:246- [Journal ] Erin M. Conlon , Joon J. Song , Jun S. Liu Bayesian models for pooling microarray studies with multiple sources of replications. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:247- [Journal ] Huiquan Wang , Craig J. Benham Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:248- [Journal ] Norbert Dojer , Anna Gambin , Andrzej Mizera , Bartek Wilczynski , Jerzy Tiuryn Applying dynamic Bayesian networks to perturbed gene expression data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:249- [Journal ] David M. Blei , K. Franks , Michael I. Jordan , I. Saira Mian Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:250- [Journal ] Martino Barenco , Jaroslav Stark , Daniel Brewer , Daniela Tomescu , Robin Callard , Michael Hubank Correction of scaling mismatches in oligonucleotide microarray data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:251- [Journal ] Yong Zhang , Shaojuan Li , Geir Skogerbø , Zhihua Zhang , Xiaopeng Zhu , Zefeng Zhang , Shiwei Sun , Hongchao Lu , Baochen Shi , Runsheng Chen Phylophenetic properties of metabolic pathway topologies as revealed by global analysis. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:252- [Journal ] Shuangge Ma , Xiao Song , Jian Huang Regularized binormal ROC method in disease classificationusing microarray data. [Citation Graph (0, 0)][DBLP ] BMC Bioinformatics, 2006, v:7, n:, pp:253- [Journal ]